<p>Polygenic risk scores (PRSs) quantify genetic susceptibilities, yet ancestry imbalance in genome-wide association studies (GWASs) limits the accuracy of monoracial PRSs in non-European populations. Here, we perform a multiancestry GWAS meta-analysis for lung cancer (76,953 cases and 1,886,372 controls), identifying 87 conditionally independent genome-wide significant loci, including two unreported cytobands. We use a PRS construction method, PRS-CSx, to develop a multiancestry PRS (<InlineEquation ID="IEq1"><EquationSource Format="TEX">\({{{{\rm{PRS}}}}}_{{{{\rm{MA}}}}}\)</EquationSource><EquationSource Format="MATHML"><math><msub><mrow><mi mathvariant="normal">PRS</mi></mrow><mrow><mi mathvariant="normal">MA</mi></mrow></msub></math></EquationSource></InlineEquation>) which outperforms 32 published PRSs. To enhance predictive power, we construct a multitrait PRS (<InlineEquation ID="IEq2"><EquationSource Format="TEX">\({{{{\rm{PRS}}}}}_{{{{\rm{MT}}}}}\)</EquationSource><EquationSource Format="MATHML"><math><msub><mrow><mi mathvariant="normal">PRS</mi></mrow><mrow><mi mathvariant="normal">MT</mi></mrow></msub></math></EquationSource></InlineEquation>) using CatBoost, integrating 32 cross-trait PRSs across three ancestries. Combining <InlineEquation ID="IEq3"><EquationSource Format="TEX">\({{{{\rm{PRS}}}}}_{{{{\rm{MA}}}}}\)</EquationSource><EquationSource Format="MATHML"><math><msub><mrow><mi mathvariant="normal">PRS</mi></mrow><mrow><mi mathvariant="normal">MA</mi></mrow></msub></math></EquationSource></InlineEquation> and <InlineEquation ID="IEq4"><EquationSource Format="TEX">\({{{{\rm{PRS}}}}}_{{{{\rm{MT}}}}}\)</EquationSource><EquationSource Format="MATHML"><math><msub><mrow><mi mathvariant="normal">PRS</mi></mrow><mrow><mi mathvariant="normal">MT</mi></mrow></msub></math></EquationSource></InlineEquation>, we generate <InlineEquation ID="IEq5"><EquationSource Format="TEX">\({{{{\rm{PRS}}}}}_{{{{\rm{MAMT}}}}}\)</EquationSource><EquationSource Format="MATHML"><math><msub><mrow><mi mathvariant="normal">PRS</mi></mrow><mrow><mi mathvariant="normal">MAMT</mi></mrow></msub></math></EquationSource></InlineEquation> and validate it in independent cohorts (OncoArray, TRICL and All of Us). <InlineEquation ID="IEq6"><EquationSource Format="TEX">\({{{{\rm{PRS}}}}}_{{{{\rm{MAMT}}}}}\)</EquationSource><EquationSource Format="MATHML"><math><msub><mrow><mi mathvariant="normal">PRS</mi></mrow><mrow><mi mathvariant="normal">MAMT</mi></mrow></msub></math></EquationSource></InlineEquation> demonstrates superior discriminability in European, Asian, and African populations, improves risk stratification, and identifies approximately 10% additional lung cancer cases in the UK Biobank. Individuals with elevated PLCO<sub>m2012</sub> scores and high genetic risk exhibit a 12.64-fold higher cumulative risk than those with low scores and low genetic risk, supporting precision prevention strategies.</p>

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Development and validation of a multiancestry and multitrait polygenic risk score for lung cancer

  • Yixin Zhang,
  • Jinglan Dai,
  • Pan Gu,
  • Yang Zhao,
  • David C. Christiani,
  • Feng Chen,
  • Sipeng Shen

摘要

Polygenic risk scores (PRSs) quantify genetic susceptibilities, yet ancestry imbalance in genome-wide association studies (GWASs) limits the accuracy of monoracial PRSs in non-European populations. Here, we perform a multiancestry GWAS meta-analysis for lung cancer (76,953 cases and 1,886,372 controls), identifying 87 conditionally independent genome-wide significant loci, including two unreported cytobands. We use a PRS construction method, PRS-CSx, to develop a multiancestry PRS (\({{{{\rm{PRS}}}}}_{{{{\rm{MA}}}}}\)PRSMA) which outperforms 32 published PRSs. To enhance predictive power, we construct a multitrait PRS (\({{{{\rm{PRS}}}}}_{{{{\rm{MT}}}}}\)PRSMT) using CatBoost, integrating 32 cross-trait PRSs across three ancestries. Combining \({{{{\rm{PRS}}}}}_{{{{\rm{MA}}}}}\)PRSMA and \({{{{\rm{PRS}}}}}_{{{{\rm{MT}}}}}\)PRSMT, we generate \({{{{\rm{PRS}}}}}_{{{{\rm{MAMT}}}}}\)PRSMAMT and validate it in independent cohorts (OncoArray, TRICL and All of Us). \({{{{\rm{PRS}}}}}_{{{{\rm{MAMT}}}}}\)PRSMAMT demonstrates superior discriminability in European, Asian, and African populations, improves risk stratification, and identifies approximately 10% additional lung cancer cases in the UK Biobank. Individuals with elevated PLCOm2012 scores and high genetic risk exhibit a 12.64-fold higher cumulative risk than those with low scores and low genetic risk, supporting precision prevention strategies.